Locus 5428

Sequence ID	2R_DroMel_CAF1
Location	17,481,428 – 17,481,614
Length	186
Max. P	0.732698

overview

Window 8

Location	17,481,428 – 17,481,546
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	81.42
Mean single sequence MFE	-33.40
Consensus MFE	-17.92
Energy contribution	-19.32
Covariance contribution	1.40
Combinations/Pair	1.16
Mean z-score	-2.13
Structure conservation index	0.54
SVM decision value	0.32
SVM RNA-class probability	0.688938
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17481428 118 + 20766785
UAUCAACCUGGAGGCGGAACCAAGGUGAGUUAUGGGUUUUUCUGGGCUUACAAUUCGGAAGAUAAGAAUUGGAUUGCAAAAAAAAACCCAAUUCAUCUUCAGAGACUGCCAUUCUCUC
.........((((((((....(((((((((..(((((((((.(..((...((((((.........))))))....))..).))))))))))))))))))......))))).))).... ( -35.40)
>DroSec_CAF1 9550 114 + 1
UAUCAACCUGGAGGCGGAACCAAGGUGAGUUCUGGGUUUUUCUGGGUUUACAAUUCGUAAGAUAAGAGAUGGAUUGCAAAA--AAACCCAAUUCAUCUUCAGAGACUGCC--UCUCAC
.........((((((((....(((((((((..(((((((((.((......((((((((..........)))))))))).))--))))))))))))))))......)))))--)))... ( -35.30)
>DroSim_CAF1 21664 115 + 1
UAUCAACCUGGAGGCGGAACCAAGGUGAGUUCUGGGUUUUUCUGGGUUUACAAUUCGUAAGAUAAGAGAUGGAGUGCAAAA-AAAACCCAUUUCAUCUAUAGAGACUGCC--UCUCAC
.........((((((((((((.....).))))).(((((((.(((((.......((....))...(((((((.((......-...)))))))))))))).))))))))))--)))... ( -33.00)
>DroEre_CAF1 12066 115 + 1
UCUCAACCUGGAGGCGGAACCAAGGUGAGUUCUUGUUUUUCCCUGAAAUACAAUUCAGAAGAUAAGAGCUGGCUUCGGGA---AUACUCAAUUCAUUCUCAGAGACUGCCUUUCUGUC
.....((..((((((((..((.((((.((((((((((((...(((((......))))))))))))))))).)))).))((---((.....))))...........))))))))..)). ( -36.50)
>DroYak_CAF1 17648 107 + 1
UCUCAAUCUGGAGGCGGAGCCACGGUGAGUUCUUGGUUUUUC--------CAAUUCGGAAGAUAAGAGUUGGAUUGCAAA---AUUCCCCAUUCAUCUUCAGAGAAUGCCUAUCUGUC
......(((((((..(((.....((.(((((....((...((--------((((((.........))))))))..))..)---))))))..)))..)))))))............... ( -26.80)
>consensus
UAUCAACCUGGAGGCGGAACCAAGGUGAGUUCUGGGUUUUUCUGGGUUUACAAUUCGGAAGAUAAGAGAUGGAUUGCAAAA__AAACCCAAUUCAUCUUCAGAGACUGCC__UCUCUC
.........((((((((((((.(((.....))).))))...............(((.((((((..(((((((...............))))))))))))).))).)))))..)))... (-17.92 = -19.32 +   1.40)

alignment

secondary structure

dotplot

Window 9

Location	17,481,506 – 17,481,614
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.02
Mean single sequence MFE	-22.04
Consensus MFE	-13.79
Energy contribution	-14.75
Covariance contribution	0.96
Combinations/Pair	1.17
Mean z-score	-1.86
Structure conservation index	0.63
SVM decision value	0.43
SVM RNA-class probability	0.732698
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17481506 108 + 20766785
AAAAAAAACCCAAUUCAUCUUCAGAGACUGCCAUUCUCUCUAUAU--------AUUGGCCUUUUGGUAUGGAGCUGGCUCCAUGCAGAUAAAA----UGAAACCUUAUAUCUUUGUUUGU
.....................((((((..((((............--------..))))......((((((((....))))))))........----............))))))..... ( -21.74)
>DroSec_CAF1 9628 104 + 1
AAA--AAACCCAAUUCAUCUUCAGAGACUGCC--UCUCACUAUGU--------AUGGGCCUUUUGGUAUGGAGCUUGCUGCAUACAGAUAAAA----UGAAACCCUAUAUCUUUGUUUGU
(((--(..((((...(((....((((.....)--)))....))).--------.))))..)))).(((((.((....)).)))))(((((...----..........)))))........ ( -18.22)
>DroSim_CAF1 21742 105 + 1
AAA-AAAACCCAUUUCAUCUAUAGAGACUGCC--UCUCACUAUGU--------AUGGGCCUUUUGGUAUGGAGCUUGCUCCAUACAGAUAAAA----UGAAACCCUAUAUCUUUGUUUGU
.((-((..(((((..(((....((((.....)--)))....))).--------)))))..)))).((((((((....))))))))(((((...----..........)))))........ ( -24.62)
>DroEre_CAF1 12144 108 + 1
GA---AUACUCAAUUCAUUCUCAGAGACUGCCUUUCUGUCUAUAU--------AUAGGCCUU-UCCAAUGGAGCUUGCUCCAUACUGAUAGAAUGAAUGAAACCCCAUAUCUUUGUUUAU
..---....(((.(((((((((((.....((((............--------..))))...-....((((((....)))))).))))..)))))))))).................... ( -24.14)
>DroYak_CAF1 17718 113 + 1
AA---AUUCCCCAUUCAUCUUCAGAGAAUGCCUAUCUGUCUAUAUAUGUACAUAUAGACCUCUUAGUAUGAAGCUUGCUCCAUACUGAUAACA----UGAAACCCUAUAUCUUUGUUUAU
..---................((((((..........((((((((......))))))))...((((((((.((....)).)))))))).....----............))))))..... ( -21.50)
>consensus
AAA__AAACCCAAUUCAUCUUCAGAGACUGCC__UCUCUCUAUAU________AUAGGCCUUUUGGUAUGGAGCUUGCUCCAUACAGAUAAAA____UGAAACCCUAUAUCUUUGUUUGU
.....................((((((..((((......................))))......((((((((....))))))))........................))))))..... (-13.79 = -14.75 +   0.96)

alignment

secondary structure

dotplot

Window 0

Location	17,481,506 – 17,481,614
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.02
Mean single sequence MFE	-26.94
Consensus MFE	-12.70
Energy contribution	-13.10
Covariance contribution	0.40
Combinations/Pair	1.25
Mean z-score	-2.16
Structure conservation index	0.47
SVM decision value	0.41
SVM RNA-class probability	0.726579
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17481506 108 - 20766785
ACAAACAAAGAUAUAAGGUUUCA----UUUUAUCUGCAUGGAGCCAGCUCCAUACCAAAAGGCCAAU--------AUAUAGAGAGAAUGGCAGUCUCUGAAGAUGAAUUGGGUUUUUUUU
........(((((.((.......----)).)))))..((((((....))))))...(((((.(((((--------.(((..(((((.......)))))....))).))))).)))))... ( -22.40)
>DroSec_CAF1 9628 104 - 1
ACAAACAAAGAUAUAGGGUUUCA----UUUUAUCUGUAUGCAGCAAGCUCCAUACCAAAAGGCCCAU--------ACAUAGUGAGA--GGCAGUCUCUGAAGAUGAAUUGGGUUU--UUU
........(((((..........----...)))))(((((.((....)).))))).((((((((((.--------.(((..(.(((--(.....)))).)..)))...)))))))--))) ( -24.82)
>DroSim_CAF1 21742 105 - 1
ACAAACAAAGAUAUAGGGUUUCA----UUUUAUCUGUAUGGAGCAAGCUCCAUACCAAAAGGCCCAU--------ACAUAGUGAGA--GGCAGUCUCUAUAGAUGAAAUGGGUUUU-UUU
........(((((..........----...)))))((((((((....)))))))).(((((((((((--------.(((....(((--(.....))))....)))..)))))))))-)). ( -30.52)
>DroEre_CAF1 12144 108 - 1
AUAAACAAAGAUAUGGGGUUUCAUUCAUUCUAUCAGUAUGGAGCAAGCUCCAUUGGA-AAGGCCUAU--------AUAUAGACAGAAAGGCAGUCUCUGAGAAUGAAUUGAGUAU---UC
...............(((((((((((((((..((((.((((((....)))))).(((-...((((..--------............))))..)))))))))))))).)))).))---)) ( -26.04)
>DroYak_CAF1 17718 113 - 1
AUAAACAAAGAUAUAGGGUUUCA----UGUUAUCAGUAUGGAGCAAGCUUCAUACUAAGAGGUCUAUAUGUACAUAUAUAGACAGAUAGGCAUUCUCUGAAGAUGAAUGGGGAAU---UU
...............(((((((.----..((((((((((((((....))))))))).....(((((((((....))))))))).))))).(((((((....)).))))).)))))---)) ( -30.90)
>consensus
ACAAACAAAGAUAUAGGGUUUCA____UUUUAUCUGUAUGGAGCAAGCUCCAUACCAAAAGGCCCAU________AUAUAGAGAGA__GGCAGUCUCUGAAGAUGAAUUGGGUUU__UUU
.............(((((.................((((((((....))))))))......(((........................)))...)))))..................... (-12.70 = -13.10 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:35 2006